Sense-antisense pairs in mammals: functional and evolutionary considerations

Abstract

Background: A significant number of genes in mammalian genomes are being found to have natural antisense transcripts (NATs). These sense-antisense (S-AS) pairs are believed to be involved in several cellular phenomena.

Results: Here, we generated a catalog of S-AS pairs occurring in the human and mouse genomes by analyzing different sources of expressed sequences available in the public domain plus 122 massively parallel signature sequencing (MPSS) libraries from a variety of human and mouse tissues. Using this dataset of almost 20,000 S-AS pairs in both genomes we investigated, in a computational and experimental way, several putative roles that have been assigned to NATs, including gene expression regulation. Furthermore, these global analyses allowed us to better dissect and propose new roles for NATs. Surprisingly, we found that a significant fraction of NATs are artifacts produced by genomic priming during cDNA library construction.

Conclusion: We propose an evolutionary and functional model in which alternative polyadenylation and retroposition account for the origin of a significant number of functional S-AS pairs in mammalian genomes.

Figure 1

GLGI-MPSS amplification. GLGI amplifications for 96 MPSS antisense tags were analyzed on agarose gels stained with ethidium bromide. Note that some lanes show only a single amplified band whereas others have more than one band and sometimes a smear. A 100 bp ladder (M) was used as molecular weight marker.

Figure 2

RT-PCR analysis for the internal priming (IP) candidates in fetal liver, colon and lung total RNA. RT-PCR was conducted in DNA-free RNA previously treated with DNAse (lanes 1 and 2) and in untreated RNA, which was, therefore, contaminated with genomic DNA (gDNA; lanes 3 and 4) for each candidate in the corresponding tissue. As a control, RT-PCR was conducted in the presence (lanes 1 and 3) and absence (lanes 2 and 4) of reverse transcriptase. gDNA was used as a positive control of the PCR reaction (lane 5) and no template as a negative control (lane 6). For fetal liver, in 3 IP candidates (5, 8 and 11) the PCR products (152 bp, 153 bp and 160 bp, respectively) were observed in the treated RNA when RT was added (lane 1) or in untreated RNA independent of the RT (lanes 3 and 4). For colon, in 1 IP candidate (9) the PCR product (158 bp) was observed in the treated RNA when RT was added (lane 1) or in untreated RNA independent of the RT (lanes 3 and 4). For the remaining IP candidates (1, 2, 4, 6, 7, 10 and 12), the PCR products (214 bp, 229 bp, 207 bp, 156 bp, 227 bp, 205 bp and 234 bp, respectively) were observed only in untreated RNA independent of the RT (lanes 3 and 4). The PCR products were analyzed on 8% polyacrylamide gels with silver staining. A 100 bp ladder (M) was used as molecular weight marker. In each gel the lower fragment in lane M correspond to 100 bp.

Figure 3

Expression pattern (in a set of 31 tissues covered by MPSS) of genes belonging to all three types of S-AS pairs (3'3', 5'5'and embedded). (a) Categories are as follows: 'no expression', for S-AS pairs whose expression was not detected (see Materials and methods for details); 'single-gene expression', for S-AS pairs in which expression is observed for only one gene in the pair; 'co-expression', for pairs in which expression is seen for both genes in the pair. (b) Rate of differential expression for the set of co-expressed S-AS pairs. Ratio of sense/antisense genes in the pair is shown on the x-axis.